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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $species_info = array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ) $local_species = 'sun' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $species_info = array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ) $local_species = 'sun' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $species_info = array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ) $local_species = 'sgi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $species_info = array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ) $local_species = 'sgi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ), 'gf_id' => 'HOM05D001265', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001265' ), 'data_identifier' => 'HOM05D001265', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001265', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03100' => 'bna', 'A03p63240' => 'bna', 'A03p63620' => 'bna', 'A04p06440' => 'bna', 'A06p33920' => 'bna', 'A07p03520' => 'bna', 'A09p46110' => 'bna', 'A10p18180' => 'bna', 'Aa31LG4G14230' => 'aar', 'Aa31LG6G12470' => 'aar', 'Aa31LG8G14830' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3819' => 'aag', 'Actinidia07199' => 'ach', 'Actinidia17354' => 'ach', 'Actinidia22892' => 'ach', 'Actinidia24165' => 'ach', 'Actinidia31301' => 'ach', 'Actinidia32466' => 'ach', 'Actinidia35684' => 'ach', 'Actinidia35685' => 'ach', 'Ah.01g004710' => 'amhyb', 'Ah.02g122990' => 'amhyb', 'AL3G50490' => 'aly', 'AL5G23320' => 'aly', 'AL5G33860' => 'aly', 'AL6G33950' => 'aly', 'AL7G15670' => 'aly', 'Aqoxy1G01002' => 'aox', 'Aqoxy2G01508' => 'aox', 'Aqoxy6G01607' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3N2IZH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JAZ85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A8DX1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DJ1DNH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H9FQ65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K88H7Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QFV9XC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V82W90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WSF6G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X30FEF' => 'arhy', 'AT2G17530' => 'ath', 'AT3G44850' => 'ath', 'AT3G53030' => 'ath', 'AT4G35500' => 'ath', 'AT5G22840' => 'ath', 'ATR0665G585' => 'atr', 'ATR0807G085' => 'atr', 'Atru.chr3.126' => 'acertr', 'Atru.chr3.3425' => 'acertr', 'Atru.chr3.4059' => 'acertr', 'Atru.chr8.1673' => 'acertr', 'AUR62002053' => 'cqu', 'AUR62003742' => 'cqu', 'AUR62023975' => 'cqu', 'AUR62031773' => 'cqu', 'AUR62037904' => 'cqu', 'AUR62037905' => 'cqu', 'AUR62037906' => 'cqu', 'AUR62040158' => 'cqu', 'BcaB01g00315' => 'bca', 'BcaB02g08541' => 'bca', 'BcaB03g12415' => 'bca', 'BcaB03g16521' => 'bca', 'BcaB05g22686' => 'bca', 'BcaB08g36404' => 'bca', 'BcaC01g02912' => 'bca', 'BcaC03g13921' => 'bca', 'BcaC04g19604' => 'bca', 'BcaC05g27274' => 'bca', 'BcaC06g36287' => 'bca', 'BcaC07g39667' => 'bca', 'BcaC07g42696' => 'bca', 'BcaNung00586' => 'bca', 'BcaNung03632' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00350' => 'bna', 'BolC1t00332H' => 'bol', 'BolC2t07199H' => 'bol', 'BolC3t18104H' => 'bol', 'BolC3t18105H' => 'bol', 'BolC4t25564H' => 'bol', 'BolC7t40972H' => 'bol', 'BolC7t46544H' => 'bol', 'BolC8t50445H' => 'bol', 'BolC9t58254H' => 'bol', 'BraA01t00294Z' => 'bra', 'BraA02t05691Z' => 'bra', 'BraA03t15402Z' => 'bra', 'BraA03t15433Z' => 'bra', 'BraA04t16348Z' => 'bra', 'BraA04t16779Z' => 'bra', 'BraA07t28142Z' => 'bra', 'BraA09t40075Z' => 'bra', 'BraA10t43893Z' => 'bra', 'C01p03450' => 'bna', 'C02p11310' => 'bna', 'C03p58470' => 'bna', 'C04p39930' => 'bna', 'C07p05730' => 'bna', 'C07p61190' => 'bna', 'C08p28350' => 'bna', 'C09p53790' => 'bna', 'CAN.G1238.16' => 'can', 'CAN.G1432.25' => 'can', 'CAN.G153.13' => 'can', 'CAN.G2149.1' => 'can', 'CAN.G328.12' => 'can', 'CAN.G546.59' => 'can', 'CAN.G824.52' => 'can', 'CANSAT25G1829' => 'cansat', 'CANSAT80G1145' => 'cansat', 'CARHR107700' => 'chi', 'CARHR151190' => 'chi', 'CARHR162920' => 'chi', 'CARHR190730' => 'chi', 'CARHR243830' => 'chi', 'Carub.0003s3162' => 'cru', 'Carub.0005s1060' => 'cru', 'Carub.0005s1953' => 'cru', 'Carub.0006s2056' => 'cru', 'Carub.0007s0485' => 'cru', 'Ca_01693_v3' => 'car', 'Ca_02852_v3' => 'car', 'Ca_10765_v3' => 'car', 'Ca_11606_v3' => 'car', 'Ca_12338_v3' => 'car', 'Ca_30939_v3' => 'car', 'CBR_g21780' => 'cbr', 'Cc01_g10040' => 'ccan', 'Cc07_g11930' => 'ccan', 'CDE02G0205' => 'cde', 'CDE03G0145' => 'cde', 'CDE03G0149' => 'cde', 'CDE05G2728' => 'cde', 'CDE05G2958' => 'cde', 'CDE06G2019' => 'cde', 'Cfa007086' => 'cfa', 'Cfa016506' => 'cfa', 'Cfa022013' => 'cfa', 'Cfa023396' => 'cfa', 'Cfa023665' => 'cfa', 'Cfa023781' => 'cfa', 'Cfa024113' => 'cfa', 'Cfa024197' => 'cfa', 'Cfa024274' => 'cfa', 'Cfa024347' => 'cfa', 'Cfa026243' => 'cfa', 'Ciclev10025598m.g' => 'ccl', 'Ciclev10028130m.g' => 'ccl', 'Ciclev10028143m.g' => 'ccl', 'CiPaw.07G002100' => 'cil', 'CiPaw.08G182100' => 'cil', 'CiPaw.09G006600' => 'cil', 'CiPaw.10G003200' => 'cil', 'ClCG01G020880' => 'cla', 'ClCG02G021760' => 'cla', 'ClCG04G009660' => 'cla', 'COL.COLO4_22282' => 'col', 'COL.COLO4_22556' => 'col', 'Cpa.g.sc47.32' => 'cpa', 'Cpa.g.sc5.108' => 'cpa', 'Cpa.g.sc6.365' => 'cpa', 'Cre06.g278254' => 'cre', 'CsaV3_6G014550' => 'csa', 'CsaV3_6G040300' => 'csa', 'CsaV3_6G047840' => 'csa', 'CSS0005164' => 'camsi', 'CSS0011778' => 'camsi', 'CSS0025947' => 'camsi', 'CSS0031177' => 'camsi', 'CSS0042315' => 'camsi', 'DCAR_014306' => 'dca', 'DCAR_015492' => 'dca', 'DCAR_015493' => 'dca', 'Dinv12557' => 'din', 'Dinv12558' => 'din', 'Dinv28319' => 'din', 'Dinv29401' => 'din', 'Dinv35850' => 'din', 'Dinv37375' => 'din', 'Dinv40194' => 'din', 'Duzib093G0572' => 'dzi', 'Duzib128G1448' => 'dzi', 'Duzib147G0231' => 'dzi', 'Duzib150G1280' => 'dzi', 'Duzib168G2167' => 'dzi', 'Duzib170G0313' => 'dzi', 'Duzib187G0306' => 'dzi', 'ECA238G0514' => 'eca', 'ECA238G2191' => 'eca', 'EL10Ac6g15049' => 'bvu', 'EL10Ac7g16758' => 'bvu', 'EL10Ac9g21043' => 'bvu', 'Eucgr.A01576' => 'egr', 'Eucgr.B03905' => 'egr', 'Eucgr.I02219' => 'egr', 'FAN02G0594' => 'fan', 'FAN05G1243' => 'fan', 'FAN05G5645' => 'fan', 'FAN09G2653' => 'fan', 'FAN09G3739' => 'fan', 'FAN10G1777' => 'fan', 'FAN11G0524' => 'fan', 'FAN14G0892' => 'fan', 'FAN16G0513' => 'fan', 'FAN19G1342' => 'fan', 'FAN21G1325' => 'fan', 'FAN23G1353' => 'fan', 'FAN26G0774' => 'fan', 'FAN28G1717' => 'fan', 'FvH4_1g10250' => 'fve', 'FvH4_3g30170' => 'fve', 'FvH4_6g17420' => 'fve', 'Glyma.01G158200' => 'gma', 'Glyma.09G197700' => 'gma', 'Glyma.10G064600' => 'gma', 'Glyma.11G086500' => 'gma', 'Glyma.12G083800' => 'gma', 'Glyma.12G179900' => 'gma', 'Glyma.13G149200' => 'gma', 'Glyma.13G320900' => 'gma', 'Glyma.16G111500' => 'gma', 'Gohir.A01G210960' => 'ghi', 'Gohir.A02G178400' => 'ghi', 'Gohir.A04G067200' => 'ghi', 'Gohir.A05G084200' => 'ghi', 'Gohir.A09G086500' => 'ghi', 'Gohir.A10G099400' => 'ghi', 'Gohir.D01G199800' => 'ghi', 'Gohir.D03G001400' => 'ghi', 'Gohir.D04G105900' => 'ghi', 'Gohir.D05G087000' => 'ghi', 'Gohir.D09G086460' => 'ghi', 'Gohir.D10G088800' => 'ghi', 'Gorai.002G244400' => 'gra', 'Gorai.003G001800' => 'gra', 'Gorai.006G102900' => 'gra', 'Gorai.009G088800' => 'gra', 'Gorai.009G409800' => 'gra', 'Gorai.011G097700' => 'gra', 'GSVIVG01022292001' => 'vvi', 'GSVIVG01031427001' => 'vvi', 'GSVIVG01033742001' => 'vvi', 'HanXRQChr02g0055141' => 'han', 'HanXRQChr03g0074931' => 'han', 'HanXRQChr04g0104531' => 'han', 'HanXRQChr07g0197571' => 'han', 'HanXRQChr09g0258141' => 'han', 'HanXRQChr09g0259411' => 'han', 'HanXRQChr14g0442871' => 'han', 'HanXRQChr14g0451861' => 'han', 'HanXRQChr16g0504141' => 'han', 'Haze_03609' => 'cav', 'Haze_03614' => 'cav', 'Haze_19508' => 'cav', 'Haze_26923' => 'cav', 'Hma1.2p1_0051F.1_g029760' => 'hma', 'Hma1.2p1_0084F.1_g042970' => 'hma', 'Hma1.2p1_0085F.1_g044620' => 'hma', 'Hma1.2p1_0300F.1_g117940' => 'hma', 'Hma1.2p1_0631F.1_g192410' => 'hma', 'HPP92_020705' => 'vpl', 'HPP92_022161' => 'vpl', 'HPP92_026338' => 'vpl', 'Hund00812' => 'sun', 'Hund19693' => 'sun', 'Lalb_Chr02g0155261' => 'lal', 'Lalb_Chr05g0214831' => 'lal', 'Lalb_Chr06g0172051' => 'lal', 'Lalb_Chr09g0334361' => 'lal', 'Lalb_Chr14g0374331' => 'lal', 'Lalb_Chr16g0380101' => 'lal', 'Lalb_Chr22g0350501' => 'lal', 'Lalb_Chr24g0395051' => 'lal', 'Lj1A217G36' => 'lonja', 'Lj2A998T25' => 'lonja', 'Lj2C500T13' => 'lonja', 'Lj2g0027955' => 'lja', 'Lj3g0019704' => 'lja', 'Lj4A237G65' => 'lonja', 'Lj4g0015669' => 'lja', 'Lj5g0018591' => 'lja', 'Lsat_1_v5_gn_2_73701' => 'lsa', 'Lsat_1_v5_gn_2_96881' => 'lsa', 'Lsat_1_v5_gn_6_42481' => 'lsa', 'Lsat_1_v5_gn_8_112461' => 'lsa', 'Manes.01G155800' => 'mes', 'Manes.02G114600' => 'mes', 'Manes.08G018200' => 'mes', 'Manes.09G058200' => 'mes', 'Manes.09G061500' => 'mes', 'Manes.11G155100' => 'mes', 'Mapoly0017s0028' => 'mpo', 'MapolyY_A0040' => 'mpo', 'MBI04_g22193_MAGBIO' => 'mbi', 'MBI05_g14360_MAGBIO' => 'mbi', 'MCO10G284' => 'mco', 'MD02G1114500' => 'mdo', 'MD03G1130900' => 'mdo', 'MD11G1153400' => 'mdo', 'MD12G1100800' => 'mdo', 'MD15G1230200' => 'mdo', 'MD15G1230300' => 'mdo', 'MD17G1175500' => 'mdo', 'Medtr1g061690' => 'mtr', 'Medtr2g084555' => 'mtr', 'Medtr4g056390' => 'mtr', 'Medtr5g024270' => 'mtr', 'Medtr8g073250' => 'mtr', 'MELO3C007972.2' => 'cme', 'MELO3C021470.2' => 'cme', 'MELO3C024505.2' => 'cme', 'Migut.D02320' => 'egut', 'Migut.H02213' => 'egut', 'Migut.N02529' => 'egut', 'MSTRG.15603' => 'ama', 'MSTRG.21075' => 'ama', 'Nitab4.5_0000381g0360' => 'nta', 'Nitab4.5_0000442g0130' => 'nta', 'Nitab4.5_0000467g0070' => 'nta', 'Nitab4.5_0000680g0070' => 'nta', 'Nitab4.5_0001365g0090' => 'nta', 'Nitab4.5_0001467g0070' => 'nta', 'Nitab4.5_0006314g0040' => 'nta', 'Nitab4.5_0006314g0050' => 'nta', 'Nitab4.5_0007782g0020' => 'nta', 'Nitab4.5_0009127g0010' => 'nta', 'Nn2g13947' => 'nnu', 'Nn5g30997' => 'nnu', 'Nn6g35107' => 'nnu', 'Oeu000703.2' => 'oeu', 'Oeu023730.1' => 'oeu', 'Oeu026993.1' => 'oeu', 'Oeu035528.1' => 'oeu', 'Oeu039141.1' => 'oeu', 'Oeu039851.1' => 'oeu', 'Oeu043390.1' => 'oeu', 'Oeu045733.1' => 'oeu', 'Oeu051381.3' => 'oeu', 'Os03g0748400' => 'osa', 'Os07g0472400' => 'osa', 'Os09g0552300' => 'osa', 'Peaxi162Scf00017g00045' => 'pax', 'Peaxi162Scf00017g00411' => 'pax', 'Peaxi162Scf00121g02438' => 'pax', 'Peaxi162Scf00146g00411' => 'pax', 'Peaxi162Scf00150g00711' => 'pax', 'Peaxi162Scf00580g00011' => 'pax', 'Peaxi162Scf02095g00012' => 'pax', 'PGR004G1877' => 'pgr', 'PGR119G0858' => 'pgr', 'PGR119G1282' => 'pgr', 'PGSC0003DMG400001514' => 'stu', 'PGSC0003DMG400002693' => 'stu', 'PGSC0003DMG400007154' => 'stu', 'PGSC0003DMG400008395' => 'stu', 'PGSC0003DMG400017474' => 'stu', 'Phvul.002G117100' => 'pvu', 'Phvul.003G270500' => 'pvu', 'Phvul.005G128900' => 'pvu', 'Phvul.007G225000' => 'pvu', 'Phvul.011G088500' => 'pvu', 'Potri.004G190400' => 'ptr', 'Potri.005G102100' => 'ptr', 'Potri.006G117800' => 'ptr', 'Potri.007G063100' => 'ptr', 'Potri.009G151500' => 'ptr', 'Pp3c15_17120' => 'ppa', 'Pp3c1_7620' => 'ppa', 'Pp3c8_18340' => 'ppa', 'Pp3c9_10940' => 'ppa', 'PRCOL_00001442' => 'pco', 'Prupe.6G116000' => 'ppe', 'Prupe.7G121300' => 'ppe', 'Prupe.7G183700' => 'ppe', 'Psat0s3169g0080' => 'psa', 'Psat0s957g0040' => 'psa', 'Psat2g148000' => 'psa', 'Psat4g105400' => 'psa', 'Psat5g253840' => 'psa', 'PSO063G1495' => 'pso', 'PSO170G5812' => 'pso', 'PSO210G1498' => 'pso', 'PSO339G0727' => 'pso', 'PSO339G1825' => 'pso', 'PSO384G2360' => 'pso', 'PSO541G2764' => 'pso', 'PSO675G1212' => 'pso', 'QL01p014166' => 'qlo', 'QL06p053037' => 'qlo', 'QL07p041063' => 'qlo', 'RcHm_v2.0_Chr2g0097071' => 'rch', 'RcHm_v2.0_Chr3g0471671' => 'rch', 'RcHm_v2.0_Chr5g0055961' => 'rch', 'Rhsim04G0137000' => 'rsi', 'Rhsim04G0137100' => 'rsi', 'Rhsim08G0027000' => 'rsi', 'Rhsim10G0194300' => 'rsi', 'Rhsim10G0195000' => 'rsi', 'Rhsim13G0103400' => 'rsi', 'Sabra04G0127800' => 'sbr', 'Sabra05G0084500' => 'sbr', 'Sabra06G0092700' => 'sbr', 'Sabra09G0120000' => 'sbr', 'SalBow3G3145' => 'sbo', 'SalBow3G3274' => 'sbo', 'SalBow3G3789' => 'sbo', 'SalBow6G4696' => 'sbo', 'Sc03g0003990' => 'sci', 'Sc06g0008850' => 'sci', 'Sc06g0008860' => 'sci', 'Sc20g0005900' => 'sci', 'Sc20g0005910' => 'sci', 'Sed0001899' => 'sed', 'Sed0009837' => 'sed', 'Sed0014876' => 'sed', 'Sed0015629' => 'sed', 'Sed0017661' => 'sed', 'SEGI_00785' => 'sgi', 'SEGI_20964' => 'sgi', 'SEGI_33534' => 'sgi', 'SEGI_34728' => 'sgi', 'SEGI_35281' => 'sgi', 'SGA_v2.0_scaffold108G30970' => 'sas', 'SGA_v2.0_scaffold2G00948' => 'sas', 'SGA_v2.0_scaffold83G26433' => 'sas', 'SHI27791' => 'shi', 'SHI29533' => 'shi', 'SMO197G0021' => 'smo', 'SMO203G0262' => 'smo', 'Solyc02g038813.1' => 'sly', 'Solyc02g082550.3' => 'sly', 'Solyc06g074700.4' => 'sly', 'Solyc09g008790.4' => 'sly', 'Solyc10g085720.2' => 'sly', 'Solyc11g066650.3' => 'sly', 'Sopen02g012570' => 'spe', 'Sopen02g027230' => 'spe', 'Sopen06g031110' => 'spe', 'Sopen09g003580' => 'spe', 'Sopen10g035140' => 'spe', 'Sopen11g026380' => 'spe', 'Sp3g30890' => 'spa', 'Sp5g09290' => 'spa', 'Sp6g22580' => 'spa', 'Sp7g33280' => 'spa', 'TAR369G0709' => 'tar', 'TAR623G0811' => 'tar', 'TAR625G1202' => 'tar', 'TAR628G0351' => 'tar', 'TAR636G2286' => 'tar', 'THA.LOC104799525' => 'tha', 'THA.LOC104804297' => 'tha', 'THA.LOC104807424' => 'tha', 'THA.LOC104810887' => 'tha', 'THA.LOC104814811' => 'tha', 'THA.LOC104827495' => 'tha', 'Thecc.01G004700' => 'tca', 'Thecc.05G077900' => 'tca', 'Thecc.09G294800' => 'tca', 'Thhalv10010281m.g' => 'esa', 'Thhalv10013197m.g' => 'esa', 'Thhalv10022695m.g' => 'esa', 'Thhalv10025221m.g' => 'esa', 'TPR.G13737' => 'tpr', 'TPR.G18794' => 'tpr', 'TPR.G32361' => 'tpr', 'TPR.G33896' => 'tpr', 'TPR.G35042' => 'tpr', 'TPR.G36155' => 'tpr', 'TPR.G5653' => 'tpr', 'TWI53G0003' => 'twi', 'TWI53G0498' => 'twi', 'TWI73G0872' => 'twi', 'TWI77G0331' => 'twi', 'TWI79G1006' => 'twi', 'unitig_0.g1495' => 'ugi', 'unitig_736.g22732' => 'ugi', 'unitig_747.g21968' => 'ugi', 'unitig_747.g21969' => 'ugi', 'unitig_899.g14728' => 'ugi', 'vmacro03235' => 'vma', 'vmacro08810' => 'vma', 'vmacro18466' => 'vma', 'vmacro20606' => 'vma', 'vmacro20626' => 'vma', 'VMungo0251G3017' => 'vmu', 'VMungo0720G1821' => 'vmu', 'VMungo1080G1221' => 'vmu', 'VMungo1127G0718' => 'vmu', 'VMungo1215G2851' => 'vmu', 'Zm00001eb057180' => 'zma', 'Zm00001eb104380' => 'zma', 'Zm00001eb104850' => 'zma', 'Zm00001eb214920' => 'zma', 'Zm00001eb320030' => 'zma' ) $gf_id = 'HOM05D001265' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001265' ) $data_identifier = 'HOM05D001265' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 11, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb320030' $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